# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 21:01:51 2020
#   Inital geometry file: a 101 line input string
#   Ligand name: (1S)-3-amino-1-[3-(cyclohexylmethoxy)phenyl]propan-1-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCC[C@H](O)c1cccc(OCC2CCCCC2)c1
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 A5V  A5V  (1S)-3-amino-1-[3-(cyclohexylmethoxy)phenyl]propan-1-ol  ligand  44  19  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_A5V
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 A5V  O    O  OH1   0  -0.663   4.5683  -0.5389   1.5966
 A5V  C2   C  CH1   0  -0.037   3.6206   0.1613   0.8210
 A5V  C1   C  CH2   0  -0.474   4.2263   0.7481  -0.4535
 A5V  C    C  CH2   0  -0.273   5.3754   1.7141  -0.2019
 A5V  N    N  NH2   0  -0.801   5.8569   2.2629  -1.4626
 A5V  C3   C  CR6   0   0.149   2.4140  -0.6879   0.4782
 A5V  C15  C  CR16  0  -0.417   1.1582  -0.1040   0.4557
 A5V  C7   C  CR6   0   0.411   0.0286  -0.8361   0.0839
 A5V  C6   C  CR16  0  -0.397   0.1638  -2.1773  -0.2640
 A5V  C5   C  CR16  0  -0.226   1.4272  -2.7586  -0.2354
 A5V  C4   C  CR16  0  -0.348   2.5476  -2.0318   0.1298
 A5V  O1   O  O2    0  -0.480  -1.1383  -0.1655   0.0939
 A5V  C8   C  CH2   0  -0.156  -2.3141  -0.8067  -0.3732
 A5V  C9   C  CH1   0  -0.278  -3.4508   0.1982  -0.3592
 A5V  C14  C  CH2   0  -0.415  -3.7809   0.6868   1.0514
 A5V  C13  C  CH2   0  -0.433  -4.9476   1.6704   1.0458
 A5V  C12  C  CH2   0  -0.430  -6.1816   1.0669   0.3840
 A5V  C11  C  CH2   0  -0.431  -5.8599   0.5651  -1.0199
 A5V  C10  C  CH2   0  -0.423  -4.6913  -0.4158  -1.0089
 A5V  H1   H  HOH1  0   0.448   5.1044  -1.0890   1.0162
 A5V  H2   H  HCH1  0   0.239   3.2818   0.9922   1.4499
 A5V  H3   H  HCH2  0   0.226   4.5629  -0.0731  -1.0995
 A5V  H4   H  HCH2  0   0.240   3.4404   1.2672  -1.0080
 A5V  H5   H  HCH2  0   0.216   5.0133   2.5418   0.4150
 A5V  H6   H  HCH2  0   0.196   6.1575   1.2132   0.3824
 A5V  H7   H  HNH2  0   0.347   6.5988   2.9257  -1.2765
 A5V  H8   H  HNH2  0   0.338   6.2880   1.5230  -2.0037
 A5V  H10  H  HCR6  0   0.251   1.0403   0.9404   0.7255
 A5V  H11  H  HCR6  0   0.275  -0.6889  -2.7779  -0.5503
 A5V  H12  H  HCR6  0   0.257   1.5297  -3.8024  -0.5037
 A5V  H13  H  HCR6  0   0.237   3.5154  -2.5175   0.1379
 A5V  H14  H  HCH2  0   0.227  -2.1584  -1.1831  -1.3915
 A5V  H15  H  HCH2  0   0.214  -2.5648  -1.6655   0.2630
 A5V  H16  H  HCH1  0   0.223  -3.1439   1.0597  -0.9674
 A5V  H17  H  HCH2  0   0.206  -4.0420  -0.1792   1.6726
 A5V  H18  H  HCH2  0   0.232  -2.9061   1.1496   1.5124
 A5V  H19  H  HCH2  0   0.227  -5.1785   1.9805   2.0678
 A5V  H20  H  HCH2  0   0.209  -4.6537   2.5774   0.5065
 A5V  H21  H  HCH2  0   0.208  -6.5463   0.2316   0.9920
 A5V  H22  H  HCH2  0   0.227  -6.9905   1.8006   0.3468
 A5V  H23  H  HCH2  0   0.228  -6.7382   0.0923  -1.4653
 A5V  H24  H  HCH2  0   0.210  -5.6072   1.4166  -1.6610
 A5V  H25  H  HCH2  0   0.229  -4.4616  -0.7353  -2.0293
 A5V  H26  H  HCH2  0   0.211  -4.9784  -1.3185  -0.4563

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 A5V  C13  C14  single    1.526  0.020  1.526
 A5V  C13  C12  single    1.525  0.020  1.525
 A5V  C14  C9   single    1.529  0.020  1.529
 A5V  C12  C11  single    1.525  0.020  1.525
 A5V  C    N    single    1.457  0.020  1.457
 A5V  C    C1   single    1.522  0.020  1.522
 A5V  C9   C8   single    1.517  0.020  1.517
 A5V  C9   C10  single    1.529  0.020  1.529
 A5V  C11  C10  single    1.526  0.020  1.526
 A5V  C8   O1   single    1.418  0.020  1.418
 A5V  C1   C2   single    1.528  0.020  1.528
 A5V  C2   O    single    1.411  0.020  1.411
 A5V  C2   C3   single    1.515  0.020  1.515
 A5V  C15  C3   aromatic  1.385  0.020  1.385
 A5V  C15  C7   aromatic  1.397  0.020  1.397
 A5V  O1   C7   single    1.346  0.020  1.346
 A5V  C3   C4   aromatic  1.395  0.020  1.395
 A5V  C7   C6   aromatic  1.392  0.020  1.392
 A5V  C4   C5   aromatic  1.385  0.020  1.385
 A5V  C6   C5   aromatic  1.391  0.020  1.391
 A5V  O    H1   single    0.850  0.020  0.980
 A5V  C2   H2   single    0.970  0.020  1.090
 A5V  C1   H3   single    0.970  0.020  1.090
 A5V  C1   H4   single    0.970  0.020  1.090
 A5V  C    H5   single    0.970  0.020  1.090
 A5V  C    H6   single    0.970  0.020  1.090
 A5V  N    H7   single    0.890  0.020  1.040
 A5V  N    H8   single    0.890  0.020  1.040
 A5V  C15  H10  single    0.930  0.020  1.080
 A5V  C6   H11  single    0.930  0.020  1.080
 A5V  C5   H12  single    0.930  0.020  1.080
 A5V  C4   H13  single    0.930  0.020  1.080
 A5V  C8   H14  single    0.970  0.020  1.090
 A5V  C8   H15  single    0.970  0.020  1.090
 A5V  C9   H16  single    0.970  0.020  1.090
 A5V  C14  H17  single    0.970  0.020  1.090
 A5V  C14  H18  single    0.970  0.020  1.090
 A5V  C13  H19  single    0.970  0.020  1.090
 A5V  C13  H20  single    0.970  0.020  1.090
 A5V  C12  H21  single    0.970  0.020  1.090
 A5V  C12  H22  single    0.970  0.020  1.090
 A5V  C11  H23  single    0.970  0.020  1.090
 A5V  C11  H24  single    0.970  0.020  1.090
 A5V  C10  H25  single    0.970  0.020  1.090
 A5V  C10  H26  single    0.970  0.020  1.090

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 A5V  H1   O    C2   109.05  3.000
 A5V  H2   C2   C3   107.98  3.000
 A5V  H2   C2   C1   108.06  3.000
 A5V  C3   C2   C1   110.01  3.000
 A5V  H2   C2   O    105.58  3.000
 A5V  C3   C2   O    112.41  3.000
 A5V  C1   C2   O    112.51  3.000
 A5V  H4   C1   H3   106.09  3.000
 A5V  H4   C1   C    108.98  3.000
 A5V  H3   C1   C    109.91  3.000
 A5V  H4   C1   C2   108.69  3.000
 A5V  H3   C1   C2   108.97  3.000
 A5V  C    C1   C2   113.89  3.000
 A5V  H6   C    H5   106.32  3.000
 A5V  H6   C    N    113.40  3.000
 A5V  H5   C    N    108.20  3.000
 A5V  H6   C    C1   109.66  3.000
 A5V  H5   C    C1   108.88  3.000
 A5V  N    C    C1   110.22  3.000
 A5V  H8   N    H7   105.34  3.000
 A5V  H8   N    C    109.13  3.000
 A5V  H7   N    C    109.26  3.000
 A5V  C4   C3   C15  119.27  3.000
 A5V  C4   C3   C2   121.36  3.000
 A5V  C15  C3   C2   119.31  3.000
 A5V  H10  C15  C7   118.88  3.000
 A5V  H10  C15  C3   120.01  3.000
 A5V  C7   C15  C3   121.11  3.000
 A5V  O1   C7   C6   124.48  3.000
 A5V  C6   C7   C15  119.54  3.000
 A5V  O1   C7   C15  115.98  3.000
 A5V  H11  C6   C5   119.31  3.000
 A5V  H11  C6   C7   121.64  3.000
 A5V  C5   C6   C7   119.05  3.000
 A5V  H12  C5   C4   119.66  3.000
 A5V  H12  C5   C6   118.93  3.000
 A5V  C4   C5   C6   121.41  3.000
 A5V  H13  C4   C5   119.33  3.000
 A5V  H13  C4   C3   121.06  3.000
 A5V  C5   C4   C3   119.61  3.000
 A5V  C8   O1   C7   119.41  3.000
 A5V  H15  C8   H14  107.57  3.000
 A5V  H15  C8   C9   109.98  3.000
 A5V  H14  C8   C9   110.01  3.000
 A5V  H15  C8   O1   110.62  3.000
 A5V  H14  C8   O1   110.07  3.000
 A5V  C9   C8   O1   108.58  3.000
 A5V  H16  C9   C10  107.84  3.000
 A5V  H16  C9   C14  108.70  3.000
 A5V  C10  C9   C14  110.19  3.000
 A5V  H16  C9   C8   107.76  3.000
 A5V  C10  C9   C8   109.75  3.000
 A5V  C14  C9   C8   112.45  3.000
 A5V  H18  C14  H17  106.63  3.000
 A5V  H18  C14  C13  109.93  3.000
 A5V  H17  C14  C13  109.20  3.000
 A5V  H18  C14  C9   110.61  3.000
 A5V  H17  C14  C9   108.75  3.000
 A5V  C13  C14  C9   111.57  3.000
 A5V  H20  C13  H19  106.39  3.000
 A5V  H20  C13  C12  109.34  3.000
 A5V  H19  C13  C12  110.32  3.000
 A5V  H20  C13  C14  109.29  3.000
 A5V  H19  C13  C14  109.94  3.000
 A5V  C12  C13  C14  111.42  3.000
 A5V  H22  C12  H21  106.52  3.000
 A5V  H22  C12  C11  110.23  3.000
 A5V  H21  C12  C11  109.28  3.000
 A5V  H22  C12  C13  110.37  3.000
 A5V  H21  C12  C13  109.28  3.000
 A5V  C11  C12  C13  111.04  3.000
 A5V  H24  C11  H23  106.46  3.000
 A5V  H24  C11  C10  109.10  3.000
 A5V  H23  C11  C10  109.90  3.000
 A5V  H24  C11  C12  109.37  3.000
 A5V  H23  C11  C12  110.37  3.000
 A5V  C10  C11  C12  111.50  3.000
 A5V  H26  C10  H25  106.54  3.000
 A5V  H26  C10  C11  109.41  3.000
 A5V  H25  C10  C11  109.99  3.000
 A5V  H26  C10  C9   109.20  3.000
 A5V  H25  C10  C9   110.08  3.000
 A5V  C11  C10  C9   111.49  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 A5V  CONST_01  C6   C7   C15  C3      0.00   0.0  0
 A5V  CONST_02  C6   C5   C4   C3      0.00   0.0  0
 A5V  CONST_03  C5   C4   C3   C15     0.00   0.0  0
 A5V  CONST_04  C5   C6   C7   C15     0.00   0.0  0
 A5V  CONST_05  C4   C3   C15  C7      0.00   0.0  0
 A5V  CONST_06  C4   C5   C6   C7      0.00   0.0  0
 A5V  CONST_07  C7   C15  C3   C2    180.00   0.0  0
 A5V  CONST_08  C5   C4   C3   C2    180.00   0.0  0
 A5V  CONST_09  O1   C7   C15  C3    180.00   0.0  0
 A5V  CONST_10  O1   C7   C6   C5    180.00   0.0  0
 A5V  CONST_11  H12  C5   C4   C3    180.00   0.0  0
 A5V  CONST_12  H13  C4   C3   C15   180.00   0.0  0
 A5V  CONST_13  H11  C6   C7   C15   180.00   0.0  0
 A5V  CONST_14  H10  C15  C7   C6    180.00   0.0  0
 A5V  Var_01    C12  C13  C14  C9     55.81  30.0  1
 A5V  Var_02    C12  C11  C10  C9    -55.83  30.0  1
 A5V  Var_03    C11  C12  C13  C14   -54.78  30.0  1
 A5V  Var_04    C10  C11  C12  C13    54.84  30.0  1
 A5V  Var_05    C9   C8   O1   C7   -175.46  30.0  1
 A5V  Var_06    N    C    C1   C2   -177.81  30.0  1
 A5V  Var_07    H7   N    C    C1    178.12  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 A5V  chir_01  C2  C1   O   C3   positiv
 A5V  chir_02  C9  C14  C8  C10  negativ

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 A5V  plan-1  C2   0.020
 A5V  plan-1  C3   0.020
 A5V  plan-1  C15  0.020
 A5V  plan-1  C7   0.020
 A5V  plan-1  C6   0.020
 A5V  plan-1  C5   0.020
 A5V  plan-1  C4   0.020
 A5V  plan-1  O1   0.020
 A5V  plan-1  H10  0.020
 A5V  plan-1  H11  0.020
 A5V  plan-1  H12  0.020
 A5V  plan-1  H13  0.020

